NPZD: An NPZD Model
In simecolModels: Model collection for the simecol package

Description Usage Format Author(s) References See Also Examples

Model describing nutrients (N), phytoplankton (P), zooplankton (Z), and detritus (D).

NPZD()

An S4 object according to the odeModel specification.
The object contains the following slots:

main NPZD model specifications.
parms vector with the named parameters of the model - see code.
times simulation time and integration interval.
init vector with start values for state variables.

Karline Soetaert

Chapter 2.8.1. from the book by Soetaert and Herman, 2009. A practical guide to ecological Modelling. Using R as a simulation platform. Springer.

R-package simecol for a description of the simObj class.

# initialize model
myNPZD <- NPZD()

# show model code, parameter settings,...
print(myNPZD)

#----------------------#
# RUNNING the model:   #
#----------------------#
#  2 steps
#  first year = spinup

res   <- out(sim(myNPZD))
num          <- nrow(res)   # last element
#  step 2  : the model is reinitialised with the final conditions of previous run
init(myNPZD) <- c(PHYTO   =res$PHYTO[num],
                  ZOO     =res$ZOO[num],
                  DETRITUS=res$DETRITUS[num],
                  DIN     =res$DIN[num])

# step 2: another 2 years simulated
Times <-seq(0,730,by=1)
times(myNPZD)  <- Times
res   <- out(sim(myNPZD))

#------------------------#
# PLOTTING model output: #
#------------------------#

par(mfrow=c(2,2), oma=c(0,0,3,0))

plot (Times,res$PAR        ,type="l",lwd=2,main="PAR"        ,
      xlab="time, hours",ylab="microEinst/m2/s")
plot (Times,res$Chlorophyll,type="l",lwd=2,main="Chlorophyll",
      xlab="time, hours",ylab="microg/l")
plot (Times,res$ZOO        ,type="l",lwd=2,main="Zooplankton",
      xlab="time, hours",ylab="mmolN/m3")
plot (Times,res$DIN        ,type="l",lwd=2,main="DIN"        ,
      xlab="time, hours",ylab="mmolN/m3")

mtext(outer=TRUE,side=3,"NPZD model",cex=1.5)